[galaxy-dev] Main Galaxy Tool Shed is running the next-stable branch
Hello all, The main Galaxy Tool Shed is now running the next-stable branch ( e6813f244a2a (next-stable) tip ) in preparation for next upcoming Galaxy release. Please let us know if you encounter anything strange or broken and we'll get things fixed asap. The main Tool Shed will be updated to the stable branch when it is created for the upcoming Galaxy release. Thanks very much, Greg Von Kuster ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_2_11_0 and ggplot2
Am 29.07.2014 um 22:45 schrieb Evan Bollig: Hey Bjoern, I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the packages the depend on those versions to R 3.0 or 3.1? Yes, this would be a better idea! The variant_recalibrator tool generates an Rscript incompatible with modern versions of ggplot2, so this could be a quite involved undertaking. Oh :( ... can we somehow get an old tarball of ggplot2? Have you looked at older linux disributions, debian stable for example? I found ggplot on download_store ;) https://github.com/bgruening/download_store/blob/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz Is that old enough? Meanwhile I'll look into the download_store option. You download all of the tarballs and install them individually with R CMD INSTALL? Not really, we have a nice routine in the toolshed for such tasks: Have a look at: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10 Note: the order of the packages are important ... Ciao, Bjoern Cheers, -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning wrote: Hi Evan, do you have somehow access to this tarball? Than we can put it on https://github.com/bgruening/download_store I use that to host R packages to save them for reproducibility. Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version? I don't think so. But that depends very much on your package. Is it not possible to use a newer R version? In either case you should save all tarballs somehow to archive them! Cheers, Bjoern -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How can I populate a data_collection output ?
Hi John, Is there any documentation that explains how dataset collections work? I'd like to learn more about it. Thanks, David On Tue, Jul 29, 2014 at 3:20 PM, John Chilton wrote: > Hello Julie, > > Right now Galaxy can implicitly create collections by running a tool > that takes in a single input or a paired dataset over say a list of > inputs or a list of paired inputs but tools cannot explicitly create > dataset collections. I think Galaxy's current capabilities add a lot > of useful functionality - but say tools that take a big input and > split it into an arbitrary number of pieces or tools that > normalize/summarize N inputs simultaneously and produce N outputs > cannot be represented. A few people made some progress on this at the > recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more > people have made it clear that it is an important feature. > > Sorry. > > -John > > > On Mon, Jul 28, 2014 at 11:47 AM, julie dubois wrote: > > Hi all, > > I'm working with data_collection as type of input in xml files. but I > > use all the datasets of a collection to compute some results that I > > want to push in a "data_collection" output. > > I know how take each dataset of a data_collection input with my > > script, like this : > > > > ... > > for $f in $input > > ... > > > > where $input is defined by > collection_type=list... in the top of my xml file. > > > > But if my script produce some outputs (number of outputs not defined > > in advance), how can I populate an output as a data_collection with my > > shscript and how should I define this output in the xml ? > > > > Thanks > > Julie > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_2_11_0 and ggplot2
Hey Bjoern, I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the packages the depend on those versions to R 3.0 or 3.1? The variant_recalibrator tool generates an Rscript incompatible with modern versions of ggplot2, so this could be a quite involved undertaking. Meanwhile I'll look into the download_store option. You download all of the tarballs and install them individually with R CMD INSTALL? Cheers, -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning wrote: > Hi Evan, > > do you have somehow access to this tarball? Than we can put it on > > https://github.com/bgruening/download_store > > I use that to host R packages to save them for reproducibility. > > >> Can I install another package_r and have packages that depend on >> package_r_2_11_0 use the newer version? > > > I don't think so. But that depends very much on your package. Is it not > possible to use a newer R version? In either case you should save all > tarballs somehow to archive them! > > Cheers, > Bjoern > >> -Evan Bollig >> Research Associate | Application Developer | User Support Consultant >> Minnesota Supercomputing Institute >> 599 Walter Library >> 612 624 1447 >> e...@msi.umn.edu >> boll0...@umn.edu >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How can I populate a data_collection output ?
Hello Julie, Right now Galaxy can implicitly create collections by running a tool that takes in a single input or a paired dataset over say a list of inputs or a list of paired inputs but tools cannot explicitly create dataset collections. I think Galaxy's current capabilities add a lot of useful functionality - but say tools that take a big input and split it into an arbitrary number of pieces or tools that normalize/summarize N inputs simultaneously and produce N outputs cannot be represented. A few people made some progress on this at the recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more people have made it clear that it is an important feature. Sorry. -John On Mon, Jul 28, 2014 at 11:47 AM, julie dubois wrote: > Hi all, > I'm working with data_collection as type of input in xml files. but I > use all the datasets of a collection to compute some results that I > want to push in a "data_collection" output. > I know how take each dataset of a data_collection input with my > script, like this : > > ... > for $f in $input > ... > > where $input is defined by collection_type=list... in the top of my xml file. > > But if my script produce some outputs (number of outputs not defined > in advance), how can I populate an output as a data_collection with my > shscript and how should I define this output in the xml ? > > Thanks > Julie > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] package_r_2_11_0 and ggplot2
Hi Evan, do you have somehow access to this tarball? Than we can put it on https://github.com/bgruening/download_store I use that to host R packages to save them for reproducibility. Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version? I don't think so. But that depends very much on your package. Is it not possible to use a newer R version? In either case you should save all tarballs somehow to archive them! Cheers, Bjoern -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] package_r_2_11_0 and ggplot2
I want to install ggplot2 into package_r. The library ggplot2 is no longer available from the CRAN mirror for R v2.11.0. How do you guys handle this situation? Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error while installing DESeq-hts
Hey Greet and Bjoern,
Sorry for the troubles with dependencies during the automated installation
procedure!
I will add tool dependency file, when I get some time during this weekend
:)
Vipin | Rätsch Lab
On Tue, Jul 29, 2014 at 10:06 AM, Björn Grüning
wrote:
> Hi Geert and Vipin,
>
> I might also consider the DESeq package and the wrappers from galaxytools
> if you plan to update your wrappers.
>
> https://github.com/bgruening/galaxytools/tree/master/
> orphan_tool_dependencies/package_deseq2_1_2_10
>
> @Geert: impressive documentation! Thanks a lot for sharing!
> Bjoern
>
>
> Am 29.07.2014 um 15:54 schrieb Geert Vandeweyer:
>
> I know this is a very old entry to the mailing list, but I thought this
>> might be useful for some people.
>>
>> Recently, I set up DESeq-hts and its siblings on our galaxy instance. To
>> succeed, I performed the steps below.
>>
>> @vipin: would you consider revising the tool_dependencies.xml for these
>> tools to take these steps into account? If you're interested, I might
>> compose a preliminary version. I believe that most, if not all of these
>> settings can be automated using the tool_dependencies files.
>>
>> I did not manage to get DEXSeq working, as it throws errors on the
>> 'estimateDispersions' step in R. I'm not sure how to solve this, as it
>> gives me the same errors using the demonstration data from the pasilla
>> library, following the manual steps. (R 3.0.2, bioconductor 2.13, DEXSeq
>> 1.8). Any hints on that are welcome.
>>
>> Best,
>>
>> Geert
>>
>> ## GALAXY PACKAGES IN TOOLSHED
>> ###
>> - install the DESeq-hts tools from the main toolshed (cec4b4fb30be from
>> vipints)
>> - install R into galaxy (I used package_R_3_0_2 from iuc (50f7e1e71271))
>> - install package_scipi and package_numpi (from iuc)
>> - install package_samtools-0.1.18 (I used
>> devteam/package_samtools_0_1_18/c0f72bdba484)
>> - install htseq_count package (I used d5edaf8dc974 from lparsons)
>>
>>
>> ## INSTALL DESeq bioconductor package
>> #
>> - open R from the commandline (using the R version installed earlier !),
>> install bioconductor package 'DESeq' :
>> - source("http://bioconductor.org/biocLite.R";)
>> - biocLite('DESeq')
>> - biocLite('DESeq2')
>> - biocLite('DEXSeq') (needed extra ubuntu package
>> libcurl4-gnutls-dev for this)
>>
>>
>> ## complie samtools from source (temporary)
>> #
>> - download samtools 0.1.18 source code into a temporary location and
>> unpack
>> - compile with : "make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC"
>>
>> ## install octave
>> ###
>> - OS-dependent, ubuntu: apt-get install octave
>>
>> ## set up DESeq-hts-1.0
>> ###
>> - go to
>> //toolshed.g2.bx.psu.edu/repos/vipints/
>> deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
>>
>>
>> - run : "setup_deseq-hts.sh" and provide paths as requested.
>> - NOTE: set samtools path to the source compiled version for now
>> (shed version fails to find sam.h)!!
>> - NOTE: also add NumPy path to the SCIPY_PATH variable
>> - rest: example (available in bin/deseq_config.sh):
>> export LD_LIBRARY_PATH=
>> export ENVIRONMENT=galaxy
>> export DESEQ_VERSION=1.12.1
>> export
>> DESEQ_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/
>> vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
>>
>> export
>> DESEQ_SRC_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/
>> repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/src
>>
>> export
>> DESEQ_BIN_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/
>> repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/bin
>>
>> export INTERPRETER=octave
>> export MATLAB_BIN_PATH=
>> export MATLAB_MEX_PATH=
>> export MATLAB_INCLUDE_DIR=
>> export OCTAVE_BIN_PATH=/opt/software/octave-3.8.0/bin/octave
>> export OCTAVE_MKOCT=/opt/software/octave-3.8.0/bin/mkoctfile
>> export SAMTOOLS_DIR=/galaxy/packages_
>> sources/samtools-0.1.18_fPIC
>> #export
>> SAMTOOLS_DIR=/galaxy/galaxy_tool_binaries/samtools/0.1.18/
>> devteam/package_samtools_0_1_18/c0f72bdba484/bin/
>>
>> export PYTHON_PATH=/galaxy/galaxy_env/bin/python
>> export
>> SCIPY_PATH=/galaxy/galaxy_tool_binaries/scipy/0.12.0/
>> iuc/package_scipy_0_12/984d208b0808/lib/python/:/
>> galaxy/galaxy_tool_binaries/numpy/1.7.1/iuc/package_numpy_
>> 1_7/ef12a3a11d5b/lib/python/
>>
>> ## USE THE TOOLSHED VERSION, The one you installed bioclite
>> packages with.
>> export
>> R_PATH=/galaxy/galaxy_tool_binaries/R_3_0_2/3.0.2/iuc/
>> package_r_3_0_2/50f7e1e71271/R
>>
>>
>> - enter mex directory, run "make octave"
>> - swap SAMTOOLS_DIR in bin/deseq_config.sh to point to the toolshed
>> version of samtools 0.1.18
>>
>> ## RUN DESeq-hts-1.0 TEST
>> ##
>> enter src directory, run test from the toolconf xml file:
>> "./deseq-hts.sh ..
Re: [galaxy-dev] IE 11 issues
That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using either Chrome/Firefox or an older version of IE (10?). You might also try using IE's compatibility mode but this must be set on a per browser basis and might be tedious: https://kb.wisc.edu/page.php?id=35591 I'll update when I find out more and thanks for the report, Carl On Mon, Jul 28, 2014 at 1:24 PM, Sajdak, Doris wrote: > Hi Carl, > > > > Thanks for the help. Here’s what I get when I try to upload a new file: > > > > SCRIPT438: Object doesn't support property or method 'attachEvent' > > File: jquery.js, Line: 1514, Column: 3 > > SCRIPT5009: 'jQuery' is undefined > > File: jquery.migrate.js, Line: 6, Column: 2 > > SCRIPT5009: 'jQuery' is undefined > > File: select2.js, Line: 21, Column: 2 > > SCRIPT5007: Unable to get property 'fn' of undefined or null reference > > File: bootstrap.js, Line: 44, Column: 3 > > SCRIPT5009: '$' is undefined > > File: galaxy.base.js, Line: 52, Column: 1 > > SCRIPT5009: 'jQuery' is undefined > > File: ui.js, Line: 735, Column: 5 > > SCRIPT5009: '$' is undefined > > File: tool_runner, Line: 64, Column: 13 > > SCRIPT5007: Unable to get property 'extend' of undefined or null reference > > File: galaxy.panels.js, Line: 28, Column: 1 > > SCRIPT5002: Function expected > > File: tool_runner, Line: 80, Column: 5 > > SCRIPT438: Object doesn't support property or method 'attachEvent' > > File: root, Line: 1514, Column: 3 > > SCRIPT5002: Function expected > > File: galaxy.tools.js, Line: 9, Column: 5 > > SCRIPT70: Permission denied > > File: root, Line: 1182, Column: 2 > > SCRIPT70: Permission denied > > File: root, Line: 1182, Column: 2 > > > > I get the following when I click on the edit button next to one of the > items in my history: > > SCRIPT438: Object doesn't support property or method 'attachEvent' > > File: jquery.js, Line: 1514, Column: 3 > > SCRIPT5009: 'jQuery' is undefined > > File: jquery.migrate.js, Line: 6, Column: 2 > > SCRIPT5009: 'jQuery' is undefined > > File: select2.js, Line: 21, Column: 2 > > SCRIPT5007: Unable to get property 'fn' of undefined or null reference > > File: bootstrap.js, Line: 44, Column: 3 > > SCRIPT5009: '$' is undefined > > File: galaxy.base.js, Line: 52, Column: 1 > > SCRIPT5009: 'jQuery' is undefined > > File: ui.js, Line: 735, Column: 5 > > SCRIPT5009: 'jQuery' is undefined > > File: jquery.autocomplete.js, Line: 9, Column: 2 > > SCRIPT5009: 'jQuery' is undefined > > File: galaxy.autocom_tagging.js, Line: 20, Column: 1 > > SCRIPT5009: '$' is undefined > > File: edit, Line: 528, Column: 9 > > SCRIPT438: Object doesn't support property or method 'attachEvent' > > File: root, Line: 1514, Column: 3 > > > > This is what I get from ‘hg summary:’ > > > > parent: 12442:29ce93a13ac7 tip > > Merge stable branch. > > branch: default > > commit: 1 modified, 177 unknown > > update: (current) > > > > Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s > something wrong on my end. > > > > Thanks, > > Dori > > > > > > *From:* Carl Eberhard [mailto:carlfeberh...@gmail.com] > *Sent:* Monday, July 28, 2014 10:55 AM > *To:* Björn Grüning > *Cc:* galaxy-dev@lists.bx.psu.edu; Sajdak, Doris > *Subject:* Re: [galaxy-dev] IE 11 issues > > > > Hi, Dori > > > > Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs > in the history panel now, but in the meantime: > > - can you open the javascript console in your IE and see if any errors > are displayed when doing the two tasks you mention? > http://msdn.microsoft.com/en-us/library/ie/bg182326%28v=vs.85%29.aspx > > - What version of Galaxy does your lab use currently? (You can view the > version by using the 'hg summary' command from the directory from which > Galaxy is run) > > > > As an aside, IE has traditionally veered away from web standards and made > it difficult to program compatible sites. Recent versions of IE have become > much more standards compliant allowing us to support them well enough. > > > > Please don't hesitate to report IE (10+) bugs when using Galaxy. > > > > Thanks for the report and I'll update with my findings soon, > > Carl > > > > > > On Mon, Jul 28, 2014 at 10:42 AM, Björn Grüning > wrote: > > Hi Dori, > > the IE is not really supported. There are many issues with IE and it's > hard to deal with that. If possible please you Chrome or FF, both are > supported and tested. > > Cheers, > Bjoern > > Am 28.07.2014 um 16:40 schrieb Sajdak, Doris: > > We are having issues with using Galaxy in Internet Explorer 11 (these > work fine in Chrome & Firefox). > > > 1. The jobs queued and history doesn't display unless you refresh > the browser window. Clicking the history reload icon doesn't work. > > 2. If I click to edit something in the history
Re: [galaxy-dev] galaxy won't start
Thanks for the fast reply! I tried it in the clean environment and it works.
I somehow totally missed that step when setting this up! So do I need to add
these 2 steps to my startup script?
/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env
. ./galaxy_env/bin/activate
Thanks,
Dori
-Original Message-
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Tuesday, July 29, 2014 10:00 AM
To: Sajdak, Doris
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] galaxy won't start
Hi Dori,
If you haven't updated galaxy or manipulated the eggs at all, then it might be
an updated system python module interfering with galaxy's resolution of the
pyyaml we ship. Can you try running galaxy from an clean virtualenv?
(https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment)
If that's not it, or you'd rather try something else, I'd probably suggest
wiping out galaxy's eggs (or just moving the folder to eggs_backup or the like)
to force Galaxy to fetch all new eggs at the next restart, and see if that
resolves it.
-Dannon
On Jul 29, 2014, at 9:40 AM, Sajdak, Doris wrote:
> I'm suddenly getting this error today when I tried to restart Galaxy:
>
> Starting galaxy...
> Some eggs are out of date, attempting to fetch...
> Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be
> fetched Fetched
> http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
> One of Galaxy's managed eggs depends on something which is missing, this is
> almost certainly a bug in the egg distribution.
> Dependency "bioblend" requires "pyyaml"
> Traceback (most recent call last):
> File "./scripts/fetch_eggs.py", line 37, in
> c.resolve() # Only fetch eggs required by the config
> File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345,
> in resolve
> egg.resolve()
> File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168,
> in resolve
> dists = pkg_resources.working_set.resolve( (
> self.distribution.as_requirement(), ), env, self.fetch )
> File "/ifs/user/galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in
> resolve
> raise VersionConflict(dist,req) # XXX put more info here
> pkg_resources.VersionConflict: (bioblend 0.4.2
> (/ifs/user/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
> Requirement.parse('pyyaml'))
>
> pyyaml is installed and I haven't updated anything that would cause a
> conflict. What do I do to fix this?
>
> Thanks,
> Dori
>
> **
> Dori Sajdak
> Senior Systems Administrator
> State University of NY at Buffalo
> Center for Computational Research
> 701 Ellicott St
> Buffalo, NY 14203
> Phone: (716) 881-8934
> Fax: (716) 849-6656
> Web: http://ccr.buffalo.edu
> **
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error while installing DESeq-hts
Hi Geert and Vipin,
I might also consider the DESeq package and the wrappers from
galaxytools if you plan to update your wrappers.
https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10
@Geert: impressive documentation! Thanks a lot for sharing!
Bjoern
Am 29.07.2014 um 15:54 schrieb Geert Vandeweyer:
I know this is a very old entry to the mailing list, but I thought this
might be useful for some people.
Recently, I set up DESeq-hts and its siblings on our galaxy instance. To
succeed, I performed the steps below.
@vipin: would you consider revising the tool_dependencies.xml for these
tools to take these steps into account? If you're interested, I might
compose a preliminary version. I believe that most, if not all of these
settings can be automated using the tool_dependencies files.
I did not manage to get DEXSeq working, as it throws errors on the
'estimateDispersions' step in R. I'm not sure how to solve this, as it
gives me the same errors using the demonstration data from the pasilla
library, following the manual steps. (R 3.0.2, bioconductor 2.13, DEXSeq
1.8). Any hints on that are welcome.
Best,
Geert
## GALAXY PACKAGES IN TOOLSHED
###
- install the DESeq-hts tools from the main toolshed (cec4b4fb30be from
vipints)
- install R into galaxy (I used package_R_3_0_2 from iuc (50f7e1e71271))
- install package_scipi and package_numpi (from iuc)
- install package_samtools-0.1.18 (I used
devteam/package_samtools_0_1_18/c0f72bdba484)
- install htseq_count package (I used d5edaf8dc974 from lparsons)
## INSTALL DESeq bioconductor package
#
- open R from the commandline (using the R version installed earlier !),
install bioconductor package 'DESeq' :
- source("http://bioconductor.org/biocLite.R";)
- biocLite('DESeq')
- biocLite('DESeq2')
- biocLite('DEXSeq') (needed extra ubuntu package
libcurl4-gnutls-dev for this)
## complie samtools from source (temporary)
#
- download samtools 0.1.18 source code into a temporary location and unpack
- compile with : "make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC"
## install octave
###
- OS-dependent, ubuntu: apt-get install octave
## set up DESeq-hts-1.0
###
- go to
//toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
- run : "setup_deseq-hts.sh" and provide paths as requested.
- NOTE: set samtools path to the source compiled version for now
(shed version fails to find sam.h)!!
- NOTE: also add NumPy path to the SCIPY_PATH variable
- rest: example (available in bin/deseq_config.sh):
export LD_LIBRARY_PATH=
export ENVIRONMENT=galaxy
export DESEQ_VERSION=1.12.1
export
DESEQ_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
export
DESEQ_SRC_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/src
export
DESEQ_BIN_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/bin
export INTERPRETER=octave
export MATLAB_BIN_PATH=
export MATLAB_MEX_PATH=
export MATLAB_INCLUDE_DIR=
export OCTAVE_BIN_PATH=/opt/software/octave-3.8.0/bin/octave
export OCTAVE_MKOCT=/opt/software/octave-3.8.0/bin/mkoctfile
export SAMTOOLS_DIR=/galaxy/packages_sources/samtools-0.1.18_fPIC
#export
SAMTOOLS_DIR=/galaxy/galaxy_tool_binaries/samtools/0.1.18/devteam/package_samtools_0_1_18/c0f72bdba484/bin/
export PYTHON_PATH=/galaxy/galaxy_env/bin/python
export
SCIPY_PATH=/galaxy/galaxy_tool_binaries/scipy/0.12.0/iuc/package_scipy_0_12/984d208b0808/lib/python/:/galaxy/galaxy_tool_binaries/numpy/1.7.1/iuc/package_numpy_1_7/ef12a3a11d5b/lib/python/
## USE THE TOOLSHED VERSION, The one you installed bioclite
packages with.
export
R_PATH=/galaxy/galaxy_tool_binaries/R_3_0_2/3.0.2/iuc/package_r_3_0_2/50f7e1e71271/R
- enter mex directory, run "make octave"
- swap SAMTOOLS_DIR in bin/deseq_config.sh to point to the toolshed
version of samtools 0.1.18
## RUN DESeq-hts-1.0 TEST
##
enter src directory, run test from the toolconf xml file:
"./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3
../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt
../test_data/genes.mat
../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam
../test_data/deseq_c_elegans_WS200-I-regions-SRX001875.bam"
## set up DESeq-hts-2.0
###
- go to
//toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_2.0
- similar to 1.0: setup config file,
- point to src compiled version of samtools
- add scipy and numpy to scipi_path variable
- use the toolshed version of R
- in mex, run "make octave"
- swap samtools path
IMPORTANT:
Re: [galaxy-dev] galaxy won't start
Hi Dori,
If you haven’t updated galaxy or manipulated the eggs at all, then it might be
an updated system python module interfering with galaxy’s resolution of the
pyyaml we ship. Can you try running galaxy from an clean virtualenv?
(https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment)
If that’s not it, or you’d rather try something else, I’d probably suggest
wiping out galaxy’s eggs (or just moving the folder to eggs_backup or the like)
to force Galaxy to fetch all new eggs at the next restart, and see if that
resolves it.
-Dannon
On Jul 29, 2014, at 9:40 AM, Sajdak, Doris wrote:
> I’m suddenly getting this error today when I tried to restart Galaxy:
>
> Starting galaxy...
> Some eggs are out of date, attempting to fetch...
> Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
> Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
> One of Galaxy's managed eggs depends on something which is missing, this is
> almost certainly a bug in the egg distribution.
> Dependency "bioblend" requires "pyyaml"
> Traceback (most recent call last):
> File "./scripts/fetch_eggs.py", line 37, in
> c.resolve() # Only fetch eggs required by the config
> File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345,
> in resolve
> egg.resolve()
> File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168,
> in resolve
> dists = pkg_resources.working_set.resolve( (
> self.distribution.as_requirement(), ), env, self.fetch )
> File "/ifs/user/galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in
> resolve
> raise VersionConflict(dist,req) # XXX put more info here
> pkg_resources.VersionConflict: (bioblend 0.4.2
> (/ifs/user/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
> Requirement.parse('pyyaml'))
>
> pyyaml is installed and I haven’t updated anything that would cause a
> conflict. What do I do to fix this?
>
> Thanks,
> Dori
>
> **
> Dori Sajdak
> Senior Systems Administrator
> State University of NY at Buffalo
> Center for Computational Research
> 701 Ellicott St
> Buffalo, NY 14203
> Phone: (716) 881-8934
> Fax: (716) 849-6656
> Web: http://ccr.buffalo.edu
> **
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
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Re: [galaxy-dev] Error while installing DESeq-hts
I know this is a very old entry to the mailing list, but I thought this
might be useful for some people.
Recently, I set up DESeq-hts and its siblings on our galaxy instance. To
succeed, I performed the steps below.
@vipin: would you consider revising the tool_dependencies.xml for these
tools to take these steps into account? If you're interested, I might
compose a preliminary version. I believe that most, if not all of these
settings can be automated using the tool_dependencies files.
I did not manage to get DEXSeq working, as it throws errors on the
'estimateDispersions' step in R. I'm not sure how to solve this, as it
gives me the same errors using the demonstration data from the pasilla
library, following the manual steps. (R 3.0.2, bioconductor 2.13, DEXSeq
1.8). Any hints on that are welcome.
Best,
Geert
## GALAXY PACKAGES IN TOOLSHED
###
- install the DESeq-hts tools from the main toolshed (cec4b4fb30be from
vipints)
- install R into galaxy (I used package_R_3_0_2 from iuc (50f7e1e71271))
- install package_scipi and package_numpi (from iuc)
- install package_samtools-0.1.18 (I used
devteam/package_samtools_0_1_18/c0f72bdba484)
- install htseq_count package (I used d5edaf8dc974 from lparsons)
## INSTALL DESeq bioconductor package
#
- open R from the commandline (using the R version installed earlier !),
install bioconductor package 'DESeq' :
- source("http://bioconductor.org/biocLite.R";)
- biocLite('DESeq')
- biocLite('DESeq2')
- biocLite('DEXSeq') (needed extra ubuntu package
libcurl4-gnutls-dev for this)
## complie samtools from source (temporary)
#
- download samtools 0.1.18 source code into a temporary location and unpack
- compile with : "make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC"
## install octave
###
- OS-dependent, ubuntu: apt-get install octave
## set up DESeq-hts-1.0
###
- go to
//toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
- run : "setup_deseq-hts.sh" and provide paths as requested.
- NOTE: set samtools path to the source compiled version for now
(shed version fails to find sam.h)!!
- NOTE: also add NumPy path to the SCIPY_PATH variable
- rest: example (available in bin/deseq_config.sh):
export LD_LIBRARY_PATH=
export ENVIRONMENT=galaxy
export DESEQ_VERSION=1.12.1
export
DESEQ_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0
export
DESEQ_SRC_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/src
export
DESEQ_BIN_PATH=/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_1.0/bin
export INTERPRETER=octave
export MATLAB_BIN_PATH=
export MATLAB_MEX_PATH=
export MATLAB_INCLUDE_DIR=
export OCTAVE_BIN_PATH=/opt/software/octave-3.8.0/bin/octave
export OCTAVE_MKOCT=/opt/software/octave-3.8.0/bin/mkoctfile
export SAMTOOLS_DIR=/galaxy/packages_sources/samtools-0.1.18_fPIC
#export
SAMTOOLS_DIR=/galaxy/galaxy_tool_binaries/samtools/0.1.18/devteam/package_samtools_0_1_18/c0f72bdba484/bin/
export PYTHON_PATH=/galaxy/galaxy_env/bin/python
export
SCIPY_PATH=/galaxy/galaxy_tool_binaries/scipy/0.12.0/iuc/package_scipy_0_12/984d208b0808/lib/python/:/galaxy/galaxy_tool_binaries/numpy/1.7.1/iuc/package_numpy_1_7/ef12a3a11d5b/lib/python/
## USE THE TOOLSHED VERSION, The one you installed bioclite
packages with.
export
R_PATH=/galaxy/galaxy_tool_binaries/R_3_0_2/3.0.2/iuc/package_r_3_0_2/50f7e1e71271/R
- enter mex directory, run "make octave"
- swap SAMTOOLS_DIR in bin/deseq_config.sh to point to the toolshed
version of samtools 0.1.18
## RUN DESeq-hts-1.0 TEST
##
enter src directory, run test from the toolconf xml file:
"./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3
../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt
../test_data/genes.mat
../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam
../test_data/deseq_c_elegans_WS200-I-regions-SRX001875.bam"
## set up DESeq-hts-2.0
###
- go to
//toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_2.0
- similar to 1.0: setup config file,
- point to src compiled version of samtools
- add scipy and numpy to scipi_path variable
- use the toolshed version of R
- in mex, run "make octave"
- swap samtools path
IMPORTANT:
- open "src/deseq2-hts.sh" in a text editor and add an extra line after
line 38 (echo load the genome annotation):
export PYTHONPATH=$PYTHONPATH:${SCIPY_PATH}
- in the same file (src/deseq2-hts.sh), append line 70
(../bin/get_read_counts...) with 2>&1 . This prevents some octave
warnings from crashing the job (
[galaxy-dev] galaxy won't start
I'm suddenly getting this error today when I tried to restart Galaxy:
Starting galaxy...
Some eggs are out of date, attempting to fetch...
Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency "bioblend" requires "pyyaml"
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 37, in
c.resolve() # Only fetch eggs required by the config
File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in
resolve
egg.resolve()
File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in
resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File "/ifs/user/galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/ifs/user/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('pyyaml'))
pyyaml is installed and I haven't updated anything that would cause a conflict.
What do I do to fix this?
Thanks,
Dori
**
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
Web: http://ccr.buffalo.edu
**
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
